Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Anna Reymer wrote: Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Hi Anna, Interesting compound you have. In addition to the link sent by Mark, I'd say that this compound is a bridge too far. It's a heavily conjugated system with transitional metal. For parameterization you should perform QM calculations, and because of the conjugation, you can't really do it "

Re: [gmx-users] producing top and gro files for the molecule with metal ions.

Anna Reymer wrote: Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/

[gmx-users] producing top and gro files for the molecule with metal ions.

Hi! I am running GROMACS for DNA with Ruthenium (II) complex. Please have a look into pdb file below. There is no parameters for any of transitional metals to produce topology and coordinates for it. The Dundee PRODRG server (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ ) has parameters on